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- PDB-4geu: Structure of a stabilised ceSAS-6 dimer -

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Basic information

Entry
Database: PDB / ID: 4geu
TitleStructure of a stabilised ceSAS-6 dimer
ComponentsSpindle assembly abnormal protein 6
KeywordsSTRUCTURAL PROTEIN / beta-sandwich / alpha-beta protein / centriolar / cytoplasmic
Function / homology
Function and homology information


centriole assembly / centriole replication / centrosome duplication / centriole / protein localization / regulation of cell cycle / protein domain specific binding / centrosome / identical protein binding / cytoplasm
Similarity search - Function
: / Centriolar protein SAS, helical domain / Spindle assembly abnormal protein 6, N-terminal domain / Dna Repair Protein Xrcc4; Chain: A, domain 1 / Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Spindle assembly abnormal protein 6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsErat, M.C. / Vakonakis, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Caenorhabditis elegans centriolar protein SAS-6 forms a spiral that is consistent with imparting a ninefold symmetry.
Authors: Hilbert, M. / Erat, M.C. / Hachet, V. / Guichard, P. / Blank, I.D. / Fluckiger, I. / Slater, L. / Lowe, E.D. / Hatzopoulos, G.N. / Steinmetz, M.O. / Gonczy, P. / Vakonakis, I.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindle assembly abnormal protein 6
B: Spindle assembly abnormal protein 6
C: Spindle assembly abnormal protein 6
D: Spindle assembly abnormal protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7556
Polymers77,4694
Non-polymers2862
Water2,396133
1
A: Spindle assembly abnormal protein 6
B: Spindle assembly abnormal protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0214
Polymers38,7342
Non-polymers2862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spindle assembly abnormal protein 6

D: Spindle assembly abnormal protein 6


Theoretical massNumber of molelcules
Total (without water)38,7342
Polymers38,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)70.580, 74.040, 81.070
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Spindle assembly abnormal protein 6


Mass: 19367.162 Da / Num. of mol.: 4 / Fragment: N-terminal head domain / Mutation: S123E, I154W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sas-6, Y45F10D.9 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O62479
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Calcium acetate hydrate, 20% (w/v) PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9687 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2012
Details: Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.65→80.19 Å / Num. all: 24219 / Num. obs: 24219 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 69.57 Å2
Reflection shellResolution: 2.65→2.79 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→80.19 Å / Cor.coef. Fo:Fc: 0.9542 / Cor.coef. Fo:Fc free: 0.9447 / SU R Cruickshank DPI: 0.488 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1221 5.09 %RANDOM
Rwork0.2001 ---
obs0.2016 23970 98.98 %-
Displacement parametersBiso mean: 90.93 Å2
Baniso -1Baniso -2Baniso -3
1--14.7215 Å20 Å2-5.0913 Å2
2--11.6543 Å20 Å2
3---3.0673 Å2
Refine analyzeLuzzati coordinate error obs: 0.584 Å
Refinement stepCycle: LAST / Resolution: 2.65→80.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4475 0 16 133 4624
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014575HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.176140HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2195SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes622HARMONIC5
X-RAY DIFFRACTIONt_it4575HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.99
X-RAY DIFFRACTIONt_other_torsion2.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion619SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4961SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.77 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2853 140 4.77 %
Rwork0.219 2797 -
all0.2221 2937 -
obs--98.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98020.504-0.47048.0542-1.23775.2005-0.0148-0.02650.12960.58490.15770.427-0.2034-0.0979-0.14290.1402-0.02420.1774-0.6407-0.0144-0.493228.50528.775836.3235
21.36920.0438-0.45866.7346-0.37579.37280.04520.0845-0.1398-0.75140.25180.42950.3441-0.3566-0.2970.23420.00220.1275-0.6639-0.0021-0.472833.4969-1.60933.4127
31.0569-0.231-0.69735.35140.71345.4812-0.0769-0.0536-0.10060.45310.3237-0.11910.20060.1638-0.24680.234-0.00680.2066-0.6419-0.0028-0.50751.843-12.8381-3.3843
41.3521-0.3879-0.53866.81971.17324.8332-0.04290.09080.1886-0.71250.3335-0.3627-0.29140.1851-0.29060.2928-0.00990.2137-0.66420.0077-0.5626-5.0748-2.391243.8217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|168 }A2 - 168
2X-RAY DIFFRACTION2{ B|2 - B|167 }B2 - 167
3X-RAY DIFFRACTION3{ C|2 - C|167 }C2 - 167
4X-RAY DIFFRACTION4{ D|2 - D|167 }D2 - 167

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